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Article ; Online: Polycyclic aromatic hydrocarbons stimulate acidogenesis, acetogenesis and methanogenesis during anaerobic co-digestion of waste activated sludge and food waste.

Chen, Yinguang / Qin, Zhiyi / Zhang, Pei / Li, Xiaolu / Feng, Leiyu

2022 Volume 360, Page(s) 127567

Abstract: Polycyclic aromatic hydrocarbons (PAHs) have been reported to influence acetic acid production during anaerobic treatment. However, investigations of the impacts of PAHs on the anaerobic co-digestion of waste activated sludge and food waste are limited. ... ...

Abstract	Polycyclic aromatic hydrocarbons (PAHs) have been reported to influence acetic acid production during anaerobic treatment. However, investigations of the impacts of PAHs on the anaerobic co-digestion of waste activated sludge and food waste are limited. Therefore, the effects of PAHs on anaerobic co-digestion were explored in this study. Four kinds of PAHs all exhibited positive contributions to methane production, especially phenanthrene. Mechanism exploration revealed that acidogenesis, acetogenesis, and methanogenesis were improved in the presence of phenanthrene, and acetotrophic methanogenesis had the greatest improvement with 69.4%. Dominant bacteria and archaea related to acetic acid and methane accumulation were changed by phenanthrene. Moreover, extracellular polymeric substances, coenzyme F
MeSH term(s)	Acetic Acid ; Anaerobiosis ; Bioreactors/microbiology ; Digestion ; Food ; Methane ; Phenanthrenes ; Polycyclic Aromatic Hydrocarbons ; Refuse Disposal ; Sewage/microbiology
Chemical Substances	Phenanthrenes ; Polycyclic Aromatic Hydrocarbons ; Sewage ; Methane (OP0UW79H66) ; Acetic Acid (Q40Q9N063P)
Language	English
Publishing date	2022-07-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2022.127567
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Article ; Online: Phenanthrene regulates metabolic pathways for hydrogen accumulation in sludge alkaline dark fermentation

Li, Xiaolu / Liu, Yin / Li, Xuyao / Qin, Zhiyi / Su, Yu / Freguia, Stefano / Feng, Leiyu / Chen, Yinguang

Bioresource Technology. 2023 Sept., v. 384 p.129311-

2023

Abstract: The influence of phenanthrene (PHE), a general polycyclic aromatic hydrocarbon in waste activated sludge, on sludge alkaline dark fermentation for hydrogen accumulation was investigated prospectively. The yield of hydrogen was 16.2 mL/g TSS with 50 mg/kg ...

Abstract	The influence of phenanthrene (PHE), a general polycyclic aromatic hydrocarbon in waste activated sludge, on sludge alkaline dark fermentation for hydrogen accumulation was investigated prospectively. The yield of hydrogen was 16.2 mL/g TSS with 50 mg/kg TSS PHE, which was 1.3-fold greater than that of the control. Mechanism research demonstrated that hydrogen production and the abundance of functional microorganisms were facilitated, whereas those of homoacetogenesis were reduced. The activity of pyruvate ferredoxin oxidoreductase in the conversion of pyruvate to reduced ferredoxin for hydrogen production was promoted by 57.2%, and that of carbon monoxide dehydrogenase and formyltetrahydrofolate synthetase, closely associated with hydrogen consumption, was suppressed by 60.5% and 55.9%, respectively. Moreover, the encoding genes involved in pyruvate metabolism were significantly up-regulated, while genes related to consuming hydrogen to reduce carbon dioxide and produce 5-methyltetrahydrofolate were down-regulated. This study notably illustrates the effect of PHE on hydrogen accumulation from metabolic pathways.
Keywords	activated sludge ; carbon dioxide ; carbon monoxide ; fermentation ; hydrogen ; hydrogen production ; phenanthrenes ; pyruvate synthase ; pyruvic acid ; BSA ; CODH ; Fd-[FeFe] ; FDH ; Fdox ; Fdred ; FTHFS ; KEGG ; PAHs ; PFOR ; PHE ; POPs ; VFAs ; WAS ; Phenanthrene ; Anaerobic fermentation ; Waste activated sludge ; Metabolic pathway
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2023.129311
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Article: Amino Acid Configuration Affects Volatile Fatty Acid Production during Proteinaceous Waste Valorization: Chemotaxis, Quorum Sensing, and Metabolism

Wang, Meng / Zhang, Xuemeng / Huang, Haining / Qin, Zhiyi / Liu, Chao / Chen, Yinguang

Environmental science & technology. 2022 May 13, v. 56, no. 12

2022

Abstract: During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In ... ...

Abstract	During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In this study, more residual d-AAs than their corresponding l-AAs were observed after VFAs were produced from kitchen waste in a pilot-scale bioreactor. For all AAs investigated, the VFA production from d-AAs was lower than that from corresponding l-AAs. The metagenomics and metaproteomics analyses revealed that the l-AA fermentation system exhibited greater bacterial chemotaxis and quorum sensing (QS) than d-AAs, which benefited the establishment of functional microorganisms (such as Clostridium, Sedimentibacter, and Peptoclostridium) and expression of functional proteins (e.g., substrate transportation cofactors, l-AA dehydrogenase, and acidogenic proteins). In addition, d-AAs need to be racemized to l-AAs before being metabolized, and the difference of VFA production between d-AAs and l-AAs decreased with the increase of racemization activity. The findings of the AA configuration affecting bacterial chemotaxis and QS, which altered microorganism communities and functional protein expression, provided a new insight into the reasons for higher l-AA metabolism than d-AAs and more d-AAs left during VFA production from proteinaceous wastes.
Keywords	Clostridium ; amino acids ; bioreactors ; biotransformation ; chemotaxis ; fermentation ; kitchen waste ; metagenomics ; oxidoreductases ; protein synthesis ; transportation ; volatile fatty acids
Language	English
Dates of publication	2022-0513
Size	p. 8702-8711.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.1c07894
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Article: Polycyclic aromatic hydrocarbons stimulate acidogenesis, acetogenesis and methanogenesis during anaerobic co-digestion of waste activated sludge and food waste

Chen, Yinguang / Qin, Zhiyi / Zhang, Pei / Li, Xiaolu / Feng, Leiyu

Bioresource technology. 2022 Sept., v. 360

2022

Abstract	Polycyclic aromatic hydrocarbons (PAHs) have been reported to influence acetic acid production during anaerobic treatment. However, investigations of the impacts of PAHs on the anaerobic co-digestion of waste activated sludge and food waste are limited. Therefore, the effects of PAHs on anaerobic co-digestion were explored in this study. Four kinds of PAHs all exhibited positive contributions to methane production, especially phenanthrene. Mechanism exploration revealed that acidogenesis, acetogenesis, and methanogenesis were improved in the presence of phenanthrene, and acetotrophic methanogenesis had the greatest improvement with 69.4%. Dominant bacteria and archaea related to acetic acid and methane accumulation were changed by phenanthrene. Moreover, extracellular polymeric substances, coenzyme F₄₂₀, and McrA gene copy number were promoted by phenanthrene, which was beneficial for the generation of acetic acid and methane. Overall, this study provides new insights into the role of organic pollutants in the anaerobic co-digestion of solid wastes.
Keywords	Archaea ; acetic acid ; activated sludge ; anaerobic digestion ; food waste ; gene dosage ; methane ; methane production ; phenanthrenes ; polymers
Language	English
Dates of publication	2022-09
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2022.127567
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Article ; Online: Amino Acid Configuration Affects Volatile Fatty Acid Production during Proteinaceous Waste Valorization: Chemotaxis, Quorum Sensing, and Metabolism.

Wang, Meng / Zhang, Xuemeng / Huang, Haining / Qin, Zhiyi / Liu, Chao / Chen, Yinguang

Environmental science & technology

2022 Volume 56, Issue 12, Page(s) 8702–8711

Abstract	During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In this study, more residual d-AAs than their corresponding l-AAs were observed after VFAs were produced from kitchen waste in a pilot-scale bioreactor. For all AAs investigated, the VFA production from d-AAs was lower than that from corresponding l-AAs. The metagenomics and metaproteomics analyses revealed that the l-AA fermentation system exhibited greater bacterial chemotaxis and quorum sensing (QS) than d-AAs, which benefited the establishment of functional microorganisms (such as
MeSH term(s)	Amino Acids/metabolism ; Anaerobiosis ; Bacteria/metabolism ; Bioreactors ; Chemotaxis ; Fatty Acids, Volatile ; Fermentation ; Hydrogen-Ion Concentration ; Proteins/metabolism ; Quorum Sensing
Chemical Substances	Amino Acids ; Fatty Acids, Volatile ; Proteins
Language	English
Publishing date	2022-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c07894
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Article ; Online: The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data.

Qin, Zhiyi / Zhang, Xuegong

PloS one

2017 Volume 12, Issue 5, Page(s) e0178320

Abstract: Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually ... ...

Abstract	Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator. We validated the method with simulation data, and applied it on RNA-seq data of 16 human body tissues and detected 3,100 switch-like exons. We found that switch-like exons tend to be more associated with Alu elements in their flanking intron regions than other types of exons.
MeSH term(s)	Alu Elements/genetics ; Exons/genetics ; Exons/physiology ; Humans ; Models, Genetic ; RNA Splice Sites/genetics ; RNA Splice Sites/physiology
Chemical Substances	RNA Splice Sites
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0178320
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Article ; Online: Phenanthrene regulates metabolic pathways for hydrogen accumulation in sludge alkaline dark fermentation.

Li, Xiaolu / Liu, Yin / Li, Xuyao / Qin, Zhiyi / Su, Yu / Freguia, Stefano / Feng, Leiyu / Chen, Yinguang

Bioresource technology

2023 Volume 384, Page(s) 129311

Abstract	The influence of phenanthrene (PHE), a general polycyclic aromatic hydrocarbon in waste activated sludge, on sludge alkaline dark fermentation for hydrogen accumulation was investigated prospectively. The yield of hydrogen was 16.2 mL/g TSS with 50 mg/kg TSS PHE, which was 1.3-fold greater than that of the control. Mechanism research demonstrated that hydrogen production and the abundance of functional microorganisms were facilitated, whereas those of homoacetogenesis were reduced. The activity of pyruvate ferredoxin oxidoreductase in the conversion of pyruvate to reduced ferredoxin for hydrogen production was promoted by 57.2%, and that of carbon monoxide dehydrogenase and formyltetrahydrofolate synthetase, closely associated with hydrogen consumption, was suppressed by 60.5% and 55.9%, respectively. Moreover, the encoding genes involved in pyruvate metabolism were significantly up-regulated, while genes related to consuming hydrogen to reduce carbon dioxide and produce 5-methyltetrahydrofolate were down-regulated. This study notably illustrates the effect of PHE on hydrogen accumulation from metabolic pathways.
MeSH term(s)	Fermentation ; Sewage ; Hydrogen/metabolism ; Phenanthrenes ; Metabolic Networks and Pathways/genetics ; Hydrogen-Ion Concentration ; Pyruvates ; Fatty Acids, Volatile ; Anaerobiosis
Chemical Substances	Sewage ; Hydrogen (7YNJ3PO35Z) ; phenanthrene (448J8E5BST) ; Phenanthrenes ; Pyruvates ; Fatty Acids, Volatile
Language	English
Publishing date	2023-06-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2023.129311
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SEASTAR: systematic evaluation of alternative transcription start sites in RNA.

Qin, Zhiyi / Stoilov, Peter / Zhang, Xuegong / Xing, Yi

Nucleic acids research

2018 Volume 46, Issue 8, Page(s) e45

Abstract: Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires ... ...

Abstract	Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.
MeSH term(s)	5' Untranslated Regions ; Alternative Splicing ; Animals ; Cell Line ; Cellular Reprogramming/genetics ; Exons ; Humans ; Induced Pluripotent Stem Cells/cytology ; Induced Pluripotent Stem Cells/metabolism ; K562 Cells ; Logistic Models ; Mice ; Promoter Regions, Genetic ; RNA Polymerase II/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Sequence Analysis, RNA/statistics & numerical data ; Software ; Transcription Initiation Site ; Transcriptome
Chemical Substances	5' Untranslated Regions ; RNA, Messenger ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2018-04-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky053
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Article: Significance of manganese resistant bacillus cereus strain WSE01 as a bioinoculant for promotion of plant growth and manganese accumulation in Myriophyllum verticillatum

Tang, Yankui / Kang, Houyao / Li, Huilan / Mo, Lihong / Qin, Zhiyi / Zhang, Kaixuan / Zhong, Yaxuan

Science of the total environment. 2020 Mar. 10, v. 707

2020

Abstract: Endophytic bacteria are generally helpful for plant growth and protection. Strain WSE01, which was identified as bacillus cereus, was isolated from the stem of Myriophyllum verticillatum and it displayed a high tolerance to Mn (1500 mg/L). The strain was ...

Abstract	Endophytic bacteria are generally helpful for plant growth and protection. Strain WSE01, which was identified as bacillus cereus, was isolated from the stem of Myriophyllum verticillatum and it displayed a high tolerance to Mn (1500 mg/L). The strain was found to be able to produce indole-3-acetic acid (IAA) and siderophores, fix the atmospheric nitrogen and dissolve potassium from insoluble K-bearing minerals. In hydroponic culture experiments, the inoculation of strain WSE01 significantly promoted the growth and increased the leaf enzyme activity in the inoculated plant M. verticillatum. Furthermore, the manganese content was increased by 36.4% in stems and by 54.7% in leaves of the inoculated plant under Mn stress at 400 mg/L, compared to the non-inoculated group. This study suggests that the strain WSE01 has the potential to be used as biocontrol and/or biofertilizing agents for application in macrophyte M. verticillatum and conduces to achieving more effective phytoremediation of metal-contaminated waters.
Keywords	Bacillus cereus ; bacteria ; biological control ; endophytes ; enzyme activity ; hydroponics ; indole acetic acid ; leaves ; macrophytes ; manganese ; minerals ; Myriophyllum ; nitrogen ; phytoremediation ; plant growth ; potassium ; siderophores ; stems
Language	English
Dates of publication	2020-0310
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2019.135867
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Article: Volatile fatty acids production from waste activated sludge during anaerobic fermentation: The effect of superfine sand

Jiang, Xiupeng / Qin, Zhiyi / Feng, Leiyu / Chen, Yinguang / Chen, Jianguang / Zhang, Xianzhong / Zhang, Zhenguang / Guo, Yingqing / Sun, Jing

Bioresource technology. 2021 Jan., v. 319

2021

Abstract: Superfine sand in waste activated sludge (WAS) increased the uncertainty of anaerobic fermentation. Experiments showed that VFAs production from WAS was positively affected by superfine sand, with an increase from 2513 mg COD/L in the control (without ... ...

Abstract	Superfine sand in waste activated sludge (WAS) increased the uncertainty of anaerobic fermentation. Experiments showed that VFAs production from WAS was positively affected by superfine sand, with an increase from 2513 mg COD/L in the control (without superfine sand) to 3002 mg COD/L with superfine sand. A mechanism study demonstrated that the main factor responsible for the improved VFAs accumulation in response to superfine sand was acetic acid, which increased by nearly 30%. Further investigation exhibited that the process of solubilization and acidification were facilitated by superfine sand and the abundance of anaerobic functional microorganisms was greatly increased. Moreover, the activities of acetate kinase (AK) as well as the quantity of AK encoding gene were greatly promoted by superfine sand. The heat release during WAS anaerobic fermentation with superfine sand was higher than that without superfine sand (25.8 × 10⁻³ versus 24.7 × 10⁻³ W·min at about 70 min).
Keywords	acetate kinase ; acetic acid ; acidification ; activated sludge ; fermentation ; genes ; heat ; sand ; solubilization ; uncertainty
Language	English
Dates of publication	2021-01
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2020.124249
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